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48-548: The APG IV system of flowering plant classification is the fourth version of a modern, mostly molecular -based, system of plant taxonomy for flowering plants (angiosperms) being developed by the Angiosperm Phylogeny Group (APG). It was published in 2016, seven years after its predecessor the APG III system was published in 2009, and 18 years after the first APG system was published in 1998. In 2009,

96-431: A percentage divergence , by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA that is sequenced. An older and superseded approach was to determine the divergences between the genotypes of individuals by DNA–DNA hybridization . The advantage claimed for using hybridization rather than gene sequencing

144-524: A constant rate of mutation, provide a molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. With the invention of Sanger sequencing in 1977, it became possible to isolate and identify these molecular structures. High-throughput sequencing may also be used to obtain the transcriptome of an organism, allowing inference of phylogenetic relationships using transcriptomic data . The most common approach

192-473: A definition similar to "all theropods closer to birds than to Deinonychus ", with Troodon being sometimes added as a second external specifier in case it is closer to birds than to Deinonychus . Avialae is also occasionally defined as an apomorphy-based clade (that is, one based on physical characteristics). Jacques Gauthier , who named Avialae in 1986, re-defined it in 2001 as all dinosaurs that possessed feathered wings used in flapping flight , and

240-442: A group called Paraves . Some basal members of Deinonychosauria, such as Microraptor , have features which may have enabled them to glide or fly. The most basal deinonychosaurs were very small. This evidence raises the possibility that the ancestor of all paravians may have been arboreal , have been able to glide, or both. Unlike Archaeopteryx and the non-avialan feathered dinosaurs, who primarily ate meat, studies suggest that

288-775: A linear arrangement of the system was published separately; the APG IV paper includes such an arrangement, cross-referenced to the 2009 one. Compared to the APG III system, the APG IV system recognizes five new orders ( Boraginales , Dilleniales , Icacinales , Metteniusales and Vahliales ), along with some new families, making a total of 64 angiosperm orders and 416 families. In general, the authors describe their philosophy as "conservative", based on making changes from APG III only where "a well-supported need" has been demonstrated. This has sometimes resulted in placements that are not compatible with published studies, but where further research

336-427: A particular species or in a group of related species, it has been found empirically that only a minority of sites show any variation at all, and most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is relatively small. In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material ; a substantial sample of individuals of

384-547: A phylogenetic tree. The third stage includes different models of DNA and amino acid substitution. Several models of substitution exist. A few examples include Hamming distance , the Jukes and Cantor one-parameter model, and the Kimura two-parameter model (see Models of DNA evolution ). The fourth stage consists of various methods of tree building, including distance-based and character-based methods. The normalized Hamming distance and

432-641: A significant complication to molecular systematics, indicating that different genes within the same organism can have different phylogenies. HGTs can be detected and excluded using a number of phylogenetic methods (see Inferring horizontal gene transfer § Explicit phylogenetic methods ). In addition, molecular phylogenies are sensitive to the assumptions and models that go into making them. Firstly, sequences must be aligned; then, issues such as long-branch attraction , saturation , and taxon sampling problems must be addressed. This means that strikingly different results can be obtained by applying different models to

480-406: A sister group, the order Crocodilia , contain the only living representatives of the reptile clade Archosauria . During the late 1990s, Aves was most commonly defined phylogenetically as all descendants of the most recent common ancestor of modern birds and Archaeopteryx lithographica . However, an earlier definition proposed by Jacques Gauthier gained wide currency in the 21st century, and

528-717: A time, sometimes for years, and rarely for life. Other species have breeding systems that are polygynous (one male with many females) or, rarely, polyandrous (one female with many males). Birds produce offspring by laying eggs which are fertilised through sexual reproduction . They are usually laid in a nest and incubated by the parents. Most birds have an extended period of parental care after hatching. Many species of birds are economically important as food for human consumption and raw material in manufacturing, with domesticated and undomesticated birds being important sources of eggs, meat, and feathers. Songbirds , parrots, and other species are popular as pets. Guano (bird excrement)

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576-575: Is a simple method; however, it is less accurate than the neighbor-joining approach. Finally, the last step comprises evaluating the trees. This assessment of accuracy is composed of consistency, efficiency, and robustness. MEGA (molecular evolutionary genetics analysis) is an analysis software that is user-friendly and free to download and use. This software is capable of analyzing both distance-based and character-based tree methodologies. MEGA also contains several options one may choose to utilize, such as heuristic approaches and bootstrapping. Bootstrapping

624-442: Is an approach that is commonly used to measure the robustness of topology in a phylogenetic tree, which demonstrates the percentage each clade is supported after numerous replicates. In general, a value greater than 70% is considered significant. The flow chart displayed on the right visually demonstrates the order of the five stages of Pevsner's molecular phylogenetic analysis technique that have been described. Molecular systematics

672-404: Is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic . This is a limitation when attempting to determine the optimal tree(s), which often involves bisecting and reconnecting portions of the phylogenetic tree(s). The recent discovery of extensive horizontal gene transfer among organisms provides

720-415: Is available at Nature Protocol. Another molecular phylogenetic analysis technique has been described by Pevsner and shall be summarized in the sentences to follow (Pevsner, 2015). A phylogenetic analysis typically consists of five major steps. The first stage comprises sequence acquisition. The following step consists of performing a multiple sequence alignment, which is the fundamental basis of constructing

768-540: Is called ornithology . Birds are feathered theropod dinosaurs and constitute the only known living dinosaurs . Likewise, birds are considered reptiles in the modern cladistic sense of the term, and their closest living relatives are the crocodilians . Birds are descendants of the primitive avialans (whose members include Archaeopteryx ) which first appeared during the Late Jurassic . According to recent estimates, modern birds ( Neornithes ) evolved in

816-482: Is examined in order to see whether the samples cluster in the way that would be expected from current ideas about the taxonomy of the group. Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a clade , which may be visually represented as the figure displayed on the right demonstrates. Statistical techniques such as bootstrapping and jackknifing help in providing reliability estimates for

864-429: Is harvested for use as a fertiliser. Birds figure throughout human culture. About 120 to 130 species have become extinct due to human activity since the 17th century, and hundreds more before then. Human activity threatens about 1,200 bird species with extinction, though efforts are underway to protect them. Recreational birdwatching is an important part of the ecotourism industry. The first classification of birds

912-989: Is needed before the classification can be changed. Key to symbols used: Like the earlier APG systems, the APG IV revision is based on a phylogenetic tree for the angiosperms, as shown below. Amborellales Nymphaeales Austrobaileyales Chloranthales Magnoliales Laurales Piperales Canellales Acorales Alismatales Petrosaviales Pandanales Dioscoreales Liliales Asparagales Arecales Poales Commelinales Zingiberales Ceratophyllales Ranunculales Proteales Trochodendrales Buxales ( continued ) Gunnerales Dilleniales Saxifragales Vitales Zygophyllales Fabales Rosales Fagales Cucurbitales Celastrales Malpighiales Oxalidales Geraniales Myrtales Crossosomatales Picramniales Sapindales Huerteales Molecular phylogenetics Molecular phylogenetics and molecular evolution correlate. Molecular evolution

960-503: Is not considered a direct ancestor of birds, though it is possibly closely related to the true ancestor. Over 40% of key traits found in modern birds evolved during the 60 million year transition from the earliest bird-line archosaurs to the first maniraptoromorphs , i.e. the first dinosaurs closer to living birds than to Tyrannosaurus rex . The loss of osteoderms otherwise common in archosaurs and acquisition of primitive feathers might have occurred early during this phase. After

1008-516: Is synonymous to Avifilopluma. † Scansoriopterygidae † Eosinopteryx † Jinfengopteryx † Aurornis † Dromaeosauridae † Troodontidae Avialae Based on fossil and biological evidence, most scientists accept that birds are a specialised subgroup of theropod dinosaurs and, more specifically, members of Maniraptora , a group of theropods which includes dromaeosaurids and oviraptorosaurs , among others. As scientists have discovered more theropods closely related to birds,

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1056-482: Is the comparison of homologous sequences for genes using sequence alignment techniques to identify similarity. Another application of molecular phylogeny is in DNA barcoding , wherein the species of an individual organism is identified using small sections of mitochondrial DNA or chloroplast DNA . Another application of the techniques that make this possible can be seen in the very limited field of human genetics, such as

1104-406: Is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. The theoretical frameworks for molecular systematics were laid in the 1960s in

1152-535: Is used by many scientists including adherents to the PhyloCode . Gauthier defined Aves to include only the crown group of the set of modern birds. This was done by excluding most groups known only from fossils , and assigning them, instead, to the broader group Avialae, on the principle that a clade based on extant species should be limited to those extant species and their closest extinct relatives. Gauthier and de Queiroz identified four different definitions for

1200-722: The Late Cretaceous and diversified dramatically around the time of the Cretaceous–Paleogene extinction event 66 million years ago, which killed off the pterosaurs and all non- ornithuran dinosaurs. Many social species preserve knowledge across generations ( culture ). Birds are social, communicating with visual signals, calls, and songs , and participating in such behaviour as cooperative breeding and hunting, flocking , and mobbing of predators. The vast majority of bird species are socially (but not necessarily sexually) monogamous , usually for one breeding season at

1248-669: The Tiaojishan Formation of China, which has been dated to the late Jurassic period ( Oxfordian stage), about 160 million years ago. The avialan species from this time period include Anchiornis huxleyi , Xiaotingia zhengi , and Aurornis xui . The well-known probable early avialan, Archaeopteryx , dates from slightly later Jurassic rocks (about 155 million years old) from Germany . Many of these early avialans shared unusual anatomical features that may be ancestral to modern birds but were later lost during bird evolution. These features include enlarged claws on

1296-476: The laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart , and a strong yet lightweight skeleton . Birds live worldwide and range in size from the 5.5 cm (2.2 in) bee hummingbird to the 2.8 m (9 ft 2 in) common ostrich . There are over 11,000 living species and they are split into 44 orders . More than half are passerine or "perching" birds. Birds have wings whose development varies according to species;

1344-529: The Jukes-Cantor correction formulas provide the degree of divergence and the probability that a nucleotide changes to another, respectively. Common tree-building methods include unweighted pair group method using arithmetic mean ( UPGMA ) and Neighbor joining , which are distance-based methods, Maximum parsimony , which is a character-based method, and Maximum likelihood estimation and Bayesian inference , which are character-based/model-based methods. UPGMA

1392-428: The appearance of Maniraptoromorpha, the next 40 million years marked a continuous reduction of body size and the accumulation of neotenic (juvenile-like) characteristics. Hypercarnivory became increasingly less common while braincases enlarged and forelimbs became longer. The integument evolved into complex, pennaceous feathers . The oldest known paravian (and probably the earliest avialan) fossils come from

1440-509: The birds that descended from them. Despite being currently one of the most widely used, the crown-group definition of Aves has been criticised by some researchers. Lee and Spencer (1997) argued that, contrary to what Gauthier defended, this definition would not increase the stability of the clade and the exact content of Aves will always be uncertain because any defined clade (either crown or not) will have few synapomorphies distinguishing it from its closest relatives. Their alternative definition

1488-665: The earliest members of Aves, is removed from this group, becoming a non-avian dinosaur instead. These proposals have been adopted by many researchers in the field of palaeontology and bird evolution , though the exact definitions applied have been inconsistent. Avialae, initially proposed to replace the traditional fossil content of Aves, is often used synonymously with the vernacular term "bird" by these researchers. † Coelurus † Ornitholestes † Ornithomimosauria † Alvarezsauridae † Oviraptorosauria   Paraves Most researchers define Avialae as branch-based clade, though definitions vary. Many authors have used

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1536-606: The ever-more-popular use of genetic testing to determine a child's paternity , as well as the emergence of a new branch of criminal forensics focused on evidence known as genetic fingerprinting . There are several methods available for performing a molecular phylogenetic analysis. One method, including a comprehensive step-by-step protocol on constructing a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment , model-test (testing best-fitting substitution models), and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference,

1584-419: The exact sequences of nucleotides or bases in either DNA or RNA segments extracted using different techniques. In general, these are considered superior for evolutionary studies, since the actions of evolution are ultimately reflected in the genetic sequences. At present, it is still a long and expensive process to sequence the entire DNA of an organism (its genome ). However, it is quite feasible to determine

1632-451: The first avialans were omnivores . The Late Jurassic Archaeopteryx is well known as one of the first transitional fossils to be found, and it provided support for the theory of evolution in the late 19th century. Archaeopteryx was the first fossil to display both clearly traditional reptilian characteristics—teeth, clawed fingers, and a long, lizard-like tail—as well as wings with flight feathers similar to those of modern birds. It

1680-523: The only known groups without wings are the extinct moa and elephant birds . Wings, which are modified forelimbs , gave birds the ability to fly, although further evolution has led to the loss of flight in some birds , including ratites , penguins , and diverse endemic island species. The digestive and respiratory systems of birds are also uniquely adapted for flight. Some bird species of aquatic environments, particularly seabirds and some waterbirds , have further evolved for swimming. The study of birds

1728-402: The outermost half) can be seen in the evolution of maniraptoromorphs, and this process culminated in the appearance of the pygostyle , an ossification of fused tail vertebrae. In the late Cretaceous, about 100 million years ago, the ancestors of all modern birds evolved a more open pelvis, allowing them to lay larger eggs compared to body size. Around 95 million years ago, they evolved

1776-486: The positions of haplotypes within the evolutionary trees. Every living organism contains deoxyribonucleic acid ( DNA ), ribonucleic acid ( RNA ), and proteins . In general, closely related organisms have a high degree of similarity in the molecular structure of these substances, while the molecules of organisms distantly related often show a pattern of dissimilarity. Conserved sequences, such as mitochondrial DNA, are expected to accumulate mutations over time, and assuming

1824-536: The previously clear distinction between non-birds and birds has become blurred. By the 2000s, discoveries in the Liaoning Province of northeast China, which demonstrated many small theropod feathered dinosaurs , contributed to this ambiguity. The consensus view in contemporary palaeontology is that the flying theropods, or avialans , are the closest relatives of the deinonychosaurs , which include dromaeosaurids and troodontids . Together, these form

1872-659: The results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of birds , for example, needed substantial revision. In the period of 1974–1986, DNA–DNA hybridization was the dominant technique used to measure genetic difference. Early attempts at molecular systematics were also termed chemotaxonomy and made use of proteins, enzymes , carbohydrates , and other molecules that were separated and characterized using techniques such as chromatography . These have been replaced in recent times largely by DNA sequencing , which produces

1920-452: The same biological name "Aves", which is a problem. The authors proposed to reserve the term Aves only for the crown group consisting of the last common ancestor of all living birds and all of its descendants, which corresponds to meaning number 4 below. They assigned other names to the other groups.   Lizards & snakes   Turtles   Crocodiles   Birds Under the fourth definition Archaeopteryx , traditionally considered one of

1968-434: The same dataset. The tree-building method also brings with it specific assumptions about tree topology, evolution speeds, and sampling. The simplistic UPGMA assumes a rooted tree and a uniform molecular clock, both of which can be incorrect. Bird Birds are a group of warm-blooded vertebrates constituting the class Aves ( Latin: [ˈaveːs] ), characterised by feathers , toothless beaked jaws,

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2016-551: The second toe which may have been held clear of the ground in life, and long feathers or "hind wings" covering the hind limbs and feet, which may have been used in aerial maneuvering. Avialans diversified into a wide variety of forms during the Cretaceous period. Many groups retained primitive characteristics , such as clawed wings and teeth, though the latter were lost independently in a number of avialan groups, including modern birds (Aves). Increasingly stiff tails (especially

2064-476: The sequence of a defined area of a particular chromosome . Typical molecular systematic analyses require the sequencing of around 1000 base pairs . At any location within such a sequence, the bases found in a given position may vary between organisms. The particular sequence found in a given organism is referred to as its haplotype . In principle, since there are four base types, with 1000 base pairs, we could have 4 distinct haplotypes. However, for organisms within

2112-423: The simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between organisms is usually re-expressed as

2160-403: The target species or other taxon is used; however, many current studies are based on single individuals. Haplotypes of individuals of closely related, yet different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: these are referred to as an outgroup . The base sequences for the haplotypes are then compared. In

2208-424: The works of Emile Zuckerkandl , Emanuel Margoliash , Linus Pauling , and Walter M. Fitch . Applications of molecular systematics were pioneered by Charles G. Sibley ( birds ), Herbert C. Dessauer ( herpetology ), and Morris Goodman ( primates ), followed by Allan C. Wilson , Robert K. Selander , and John C. Avise (who studied various groups). Work with protein electrophoresis began around 1956. Although

2256-466: Was developed by Francis Willughby and John Ray in their 1676 volume Ornithologiae . Carl Linnaeus modified that work in 1758 to devise the taxonomic classification system currently in use. Birds are categorised as the biological class Aves in Linnaean taxonomy . Phylogenetic taxonomy places Aves in the clade Theropoda as an infraclass or a subclass, more recently a subclass. Aves and

2304-398: Was that it was based on the entire genotype, rather than on particular sections of DNA. Modern sequence comparison techniques overcome this objection by the use of multiple sequences. Once the divergences between all pairs of samples have been determined, the resulting triangular matrix of differences is submitted to some form of statistical cluster analysis , and the resulting dendrogram

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